Thursday, 27 November 2014

I recently took a course in cosmology in the hope of trying
to fill some voids in my knowledge. We were spared all the mathematics that are
needed for a comprehensive understanding, but the excellent tutor certainly put
across key points on the age of the universe, its size, its changes through time,
and the features of some of its components. My knowledge remains
superficial, but it is enough for me to realise that it is impossible to get
any real sense of the distances and times involved and humans will never be
able to do this as the numbers are so large that we cannot compare them with with
anything familiar to us. Another impression that the cosmology course left with
me was that some explanations of events and structures are close to being
science fiction.

The topic that created most enthusiasm among
members of the class was discussion of the origin of life and whether living
organisms exist elsewhere. The desire to find organisms has extended to looking
for chemicals that may be involved in their make-up and we also make projections
about possible habitats; a popular one being to equate finding water on other
planets, or in other parts of the Universe, as being tantamount to finding
living organisms. We are interested especially in the possibility of
intelligent life, with which we can communicate, providing us with a feeling
that we are not alone.

It was clear that most of us in the cosmology class had
varying views on what we meant by life, with most thinking that it was only
possible in a distinct organism, perhaps consisting of one cell, perhaps of
several cells. So, is there an agreed definition? As a starting
point, I read Schrödinger’s What is Life?, based on a series of
lectures he gave at Trinity College Dublin in 1943 [1]. Schrödinger’s discourse detailed the way
in which cells, and thus multicellular organisms, were controlled by the
physics and chemistry of genes (although the mechanism of control was not known
until the structure of DNA was discovered 10 years later). I would like to
quote two sections [1]:

What is the characteristic
feature of life? When is a piece of matter said to be alive? When it goes on
‘doing something’, moving, exchanging material with its environment, and so
forth, and that for a much longer period than we would expect of an inanimate
piece of matter to ‘keep going’ under similar circumstances.

The unfolding of events in the
life cycle of an organism exhibits an admirable regularity and orderliness,
unrivalled by anything we meet in inanimate matter. We find it controlled by a
supremely well-ordered group of atoms, which represent only a very small
fraction of the sum total in every cell. Moreover, from the view we have formed
of the mechanism of mutation we conclude that the dislocation of just a few atoms
from within the group of ‘governing atoms’ of the germ cell suffices to bring
about a well-defined change in the large-scale hereditary characteristics of
the organism.

I am comfortable with Schrödinger’s view that life is a feature of organisms and that the
biology of organisms is under the control of what we now know to be DNA.
However, we still lack a definition of life and, for this, I turned to Pincock and Frary's The Origins of the Universe for Dummies.
Having reviewed complexity, metabolism, development, autonomy and reproduction,
the authors write [2]:

Taking all the elements we
describe in the previous sections, and all their shortcomings, into account, we
can come up with a simple, one-sentence definition of life. (Of course, scientists
tell you that this description isn’t perfect, but it serves as a rough
definition, at least for now.)

Here’s the working definition,
which is sometimes known as the NASA
definition of life: Life is a
self-sustaining chemical system capable of Darwinian evolution [my
emboldening].

There is no mention of organisms here and it is a definition
that is difficult for all to accept, as Pincock and Frary anticipated.

It has been pointed out that there is unlikely ever to be
agreement on a definition of life. Carol Cleland and Christopher Chyba write
[3]:

The philosophical question of the
definition of ‘life’ has increasing practical importance. As science makes
progress towards understanding the origin of life on Earth, as laboratory
experiments approach the synthesis of life (as measured by the criteria of some
definitions), and as greater attention is focused on astrobiology and the
search for life on Mars and Jupiter’s moon Europa, the utility of a general
definition grows. In particular, definitions of ‘life’ are explicit or implicit
in any remote in situ search for extraterrestrial life.

Is science making progress towards understanding the origin
of life on Earth and do laboratory experiments approach the synthesis of life? I
question whether this is so, but, as Cleland and Chyba point out, it depends on
the definition used. Does anyone consider DNA to be alive? Isn’t there an elusive essence
to life that involves more than the interaction of molecules? Isn’t that what Schrödinger implied?

Cleland and Chyba’s Abstract is worth quoting [3]:

There is no broadly accepted
definition of ‘life’ Suggested definitions face problems, often in the form of
robust counter-examples. Here we use insights from philosophical investigations
into language to argue that defining ‘life’ currently poses a dilemma analogous
to that faced by those hoping to define ‘water’ before the existence of molecular
theory. In the absence of an analogous theory of the nature of living systems,
interminable controversy over the definition of life is inescapable.

How true. One reason that I left a University astrobiology research group was because we all talked
about life, but there was no consensus on what we meant. I couldn’t sit back
and listen to colleagues talking about the origin of life when they really
meant the first appearance of RNA and DNA. I had similar problems when listening
to them, and others, saying that life probably originated in hydrothermal vents;
that extremophile microorganisms are likely to be found in extraterrestrial habitats with similar
harsh conditions to those where these extraordinary organisms live on Earth; etc. While it would be wonderful to find living cells, or conclusive
evidence of living cells having been present, on moons or planets elsewhere in
the solar system (or elsewhere in the Universe), I’m not expecting such discoveries
to be made, as I remain convinced that the first living cell formed on Earth in
a once and once only event. Isn't that the best working hypothesis until we can
prove otherwise?

Monday, 17 November 2014

The quotation in the title of this post is a translation
from Aristotle in On the Parts of Animals,
written 350 years BCE. Together with a photograph of a portrait bust, it
forms the Frontispiece for Charles Singer’s A
Short History of Biology (see above) and Singer, an avid admirer, writes:

The surviving works of Aristotle
place him as among the very greatest biologists of all time. He set himself to
cover all human knowledge, and succeeded in this vast task in a way which no
one has succeeded before or since. He was a deeply original thinker, and he had
an unrivalled capacity for arranging his own and other people’s material. To these
qualities he added first-class powers of observation and great shrewdness of
judgement. No succeeding thinker has exercised so great an influence. [1]

We are left in no doubt as to Singer’s view of Aristotle,
his qualities and his importance, but he regards Pliny the Elder, another
well-known Natural Historian from antiquity, quite differently. Pliny was Roman
and:

..a well-born gentleman, and an
able and efficient civil servant. He was a man of immense industry with an
enthusiasm for collection. He did not, however, collect natural history
objects, but only information or rather misinformation about them. He put
together a vast number of extracts from works concerning every aspect of
Nature. These he embodied in his famous book on Natural History. Unfortunately, Pliny’s judgement was in no way
comparable to his industry. He was excessively credulous. Thus his work became
a repository of tales of wonder, of travellers’ and sailors’ yarns, and of superstitions
of farmers and labourers. As such it is a very important source of information
for the customs of antiquity, though as science, judged by the standards of his
great predecessors, such as Aristotle.., it is simply laughable.

Despite the low quality of his material, Pliny’s work was widely read
during the ages which followed. He was the main source of such little natural history
as was studied for a thousand years after his time. Many common superstitions
have thus passed into current belief from Pliny.

One idea which comes down to us direct from Pliny is very commonly
encountered among ignorant people. It is the belief that every animal, plant
and mineral has some use; that is to
say, was formed for the benefit of man. [1]

This is harsh criticism, and Pliny does not benefit by comparison
with Aristotle. However, it is easy to see that Natural History is very much as Singer describes it. [2] The work is
truly encyclopaedic and does not confine itself to plants and animals, but also
to many aspects of the physical World.

The idea of the usefulness of plants and animals to
humans cannot be laid solely at Pliny’s door. In Genesis 1: 26-29 in The Holy Bible, we read: [3]

And God said, Let us make man in
our image, after our likeness: and let them have dominion over the fish of the
sea, and over the fowl of the air, and over the cattle, and over all the earth,
and over every creeping thing that creepeth upon the earth.. ..So God created
man in his own image, in the image of God created he him; male and female
created he them.. .. And God blessed them, and God said unto them, Be fruitful,
and multiply, and replenish the earth, and subdue it: and have dominion over
the fish of the sea, and over the fowl of the air, and over every living thing
that moveth upon the earth.. .. And God said, Behold, I have given you every
herb bearing seed, which is upon the face of all the earth, and every tree, in
the which is the fruit of a tree yielding seed; to you it shall be for meat..

To me, this is as anthropocentric as the writings of Pliny
and must have had a considerable effect on how Nature was regarded during the
Dark Ages. It is interesting that Singer’s statement about anthropocentricity
was made in 1931, at a time when the study of Biology was still strongly
influenced by Natural History and it was recognised that having knowledge of
plants and animals of all types was important. Since then, we have concentrated more
and more on humans, or genetic analogues of our species.

In a wider context, humans threaten not only each other but,
increasingly, the existence of other organisms and the environment. It can be
argued that the widespread extinction of plants and animals arises from our
belief that they are not important, unless they benefit us directly as crops,
saleable commodities, or sources of useful chemicals. It is not the thought of
Pliny, or of Jewish and Christian literature, that is driving this attitude,
but our politico-economic systems. Singer’s ire is even more relevant now than
it was eighty years ago and I wonder if we, like Pliny, are excessively
credulous in consuming information conveyed to us about what is really
important. It might be suggested that we should return to Aristotelian ideals,
reduce our anthropocentricity, and re-examine the view that “All Nature is
marvellous” before we become even more destructive. So how can this be achieved
in an era of sound bites, reality TV, advertising, and other challenges to our
credulity?

[1] Charles Singer (1931) A Short History of Biology. Oxford, The Clarendon Press.

Thursday, 6 November 2014

During the passage of HMS
Beagle through the eastern Atlantic, Charles Darwin became intrigued by dust
that accumulated on parts of the ship:

On the 16th of January (1833),
when the Beagle was ten miles off the N.W. end of St. Jago [Santiago, Cape
Verde Islands], some very fine dust was found adhering to the under side of the
horizontal wind-vane at the mast-head; it appeared to have been filtered by the
gauze from the air, as the ship lay inclined to the wind. The wind had been for
twenty-four hours previously E.N.E., and hence, from the position of the ship,
the dust probably came from the coast of Africa. The atmosphere was so hazy
that the visible horizon was only one mile distant.. [1]

..Many scattered accounts have
appeared concerning the dust which has fallen in considerable quantities on
vessels on the African side of the Atlantic Ocean. It has appeared to me
desirable to collect these accounts, more especially since Professor
Ehrenberg’s remarkable discovery that the dust consists in considerable part of
Infusoria and Phytolitharia [the remains of the coverings of single-celled
organisms, the latter with siliceous coats].. [1]

..it is a very singular fact,
that out of the many forms [of the coverings of single-celled organisms] known
to Professor Ehrenberg as characteristic of Africa, and more especially of the
Sahara and Senegambian regions, none were found in the dust. From these facts
one might at first doubt whether the dust came from Africa; but considering
that it has invariably fallen with the wind between N.E. and S.E., that is,
directly from the coast of Africa; that the first commencement of the haze has
been seen to come on with these winds; that coarser particles have first
fallen; that the dust and hazy atmosphere is more common near the African coast
than further in the Atlantic; and lastly, that the months during whichit falls coincide with those when the
harmattan blows from the continent, and when it is known that clouds of dust
and sand are raised by it, I think there can be no doubt that the dust which
falls in the Atlantic does come from Africa. [1]

We know from satellite images that considerable amounts of
dust are carried out far into the Atlantic, on to South America [2] and, with
changes in the jet stream and other meteorological events, to many other parts
of the Earth (see image below). It is intriguing to read in Darwin’s report
that the dust contains the identifiable remains of “Infusoria and Phytolitharia”. The northern
part of Africa, where these aquatic organisms originated, is now desert, but
there must clearly have been water present in earlier times and, indeed, a lake
covering 350,000 km2 existed in the region 6,000 years ago. [3] It
is likely that the remains of cells that Darwin, and others, recorded from the
Atlantic were originally from this source and we now know that components of
the dust include residues from many other algae and animals, including fish,
and that these fall into the water, or are carried there by rains, and act as fertilisers. [3]

Anyone who gardens knows that fish bone meal is a good
source of phosphorus for growing plants and it is thus likely to play a similar
role when deposited into the oceans, or on to terrestrial landscapes. Recent research
by Karen Hudson-Edwards and colleagues [3] has shown that the mineral residues
of fish bones allow easier solution of phosphorus than many other bound organic
residues that are present in the dust being blown from the Sahara. There is, of
course, a finite amount of this material and, in time, it will form a smaller
and smaller fraction of that eroded from the region, as the strata
containing the organic remains begin to disappear.

Many people are familiar with the idea of fish, and other
animals, falling from the sky, having been sucked up by waterspouts from surface
waters, [4] but the rain-down of fossilised fish bone meal, and other
mineralised plant and animal material, is less well-known. It has been, and continues
to be, an important input of fertiliser to both aquatic and terrestrial
communities.

[1] Charles Darwin (1846) An account of the Fine Dust which
often falls on Vessels in the Atlantic Ocean. Quarterly Journal of the Geological Society 2: 26-30.